Hi all,

In Pipeline Pilot 2022 SP1 there is a protocol called "Binding Energy with MM-PBSA". In this protocol, the subprotocol called "Assign Forcefield Types" has an option under the "Advanced" parameters that reads "Add Hydrogens". The description of this option is: "Add forcefield hydrogens to the molecule prior to forcefield assignment." and I am not sure what that means. If the input macromolecule in PDB format is already curated, with the hydrogens added as desired, will this "Add Hydrogens" option set to True change the input structures in any way? Or does it keep the structure intact, as given via the input, but assigns force field parameters to hydrogens that are compatible with the CHARMm naming conventions?

Many thanks for the help!

Agis